Sorry to revive this old thread, but it is worth posting that the original problem has now been solved. Mobi and azw3 files store toc links as offsets. Both Calibre and Kindleunpack assumed that the offset will point to a tag with an id attribute, which they used as an "anchor" for the TOC entries when converting. However, it has recently become apparent that for some books this assumption is incorrect. With these books, the converted TOC entries would point to the file as a whole and not to any particular point in the file.
Kovid has fixed this in Calibre and KevinH has indicated that an update of Kindleunpack this coming weekend will also contain a fix. You will need to reconvert any affected books to epub from the original mobi or azw3 file.
This is all documented in this thread:
https://www.mobileread.com/forums/sho...d.php?t=259557